Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_002876377.1 B506_RS00085 aldehyde dehydrogenase family protein
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_000387565.1:WP_002876377.1 Length = 464 Score = 194 bits (494), Expect = 4e-54 Identities = 125/406 (30%), Positives = 208/406 (51%), Gaps = 16/406 (3%) Query: 36 IFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGRVED 95 I+++++ V + EA + E +++ I + +NAR LA++A ETGRG+VED Sbjct: 19 IYHNIDILVNKSHEALAQMDDFSQEDVDKLCQVIEKVGEDNARYLAQMAVDETGRGKVED 78 Query: 96 KVAKNILAAKKTPGTEDLKPTAWTG----DRGLTLVEMA-PVGVIASITPVTNPTATIIN 150 KV KN AA+ E +K G D+ L+++A P+GVIA +TPVTNPT+T+I Sbjct: 79 KVTKNTYAAQTI--WESMKDMKTVGVIEEDKQEGLMKIAEPIGVIAGVTPVTNPTSTVIF 136 Query: 151 NTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLM 210 + + + N ++F HP A+K + ++I EA + GAP + I +P++ LM Sbjct: 137 KAMIAMKSKNTIIFGFHPQAQKCCVETAKLIKEATVAAGAPENWIQWIEHPSLTATTALM 196 Query: 211 EHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDN 270 +P+V +V+ TGG +V+ A GK +G G GN P +++TADI ++ +DI +FDN Sbjct: 197 NNPKVQIVLATGGPGMVKAAYSTGKPALGVGPGNGPSYIEKTADIEQSVNDIVLSKTFDN 256 Query: 271 NLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIF--QGGAINKDLIGRD 328 + C +E ++ + + D + E + Y L +I E + G + + G+ Sbjct: 257 GMICASENSVVVDKEVYDQVKEAFLKRHCYFLKADEIKLFEEHFIDPRRGTVAGPMAGKS 316 Query: 329 AHFILSQIGIETGKDIRLVVMP---VDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAVKA 385 A I G+ D +++V V +PL E+L PV +A + Sbjct: 317 AVKIAEMCGVTVPADTQVIVAEYSGVGPKYPL-SAEKLSPVFTLYKAENSAQAFKICTDL 375 Query: 386 --EGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGG 429 GG HTA +H++N + + FA A+ + N+P+ G G GG Sbjct: 376 LNYGGRGHTAGIHTQNSKVIRKFAFAMSACRILVNSPAALG-GIGG 420 Lambda K H 0.317 0.133 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 489 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 464 Length adjustment: 33 Effective length of query: 433 Effective length of database: 431 Effective search space: 186623 Effective search space used: 186623 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory